DAC CTC - Plasma-DNA

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Ellen Heitzer
ellen.heitzer@medunigraz.at

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This DAC controls 44 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000220	Deep sequencing of CTCs	454 GS FLX Titanium Illumina MiSeq	3
EGAD00001000224	Enrichment of CRC	454 GS FLX Titanium	2
EGAD00001000225	Deep sequencing of KRAS	454 GS FLX Titanium	8
EGAD00001000364	We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).	Illumina MiSeq	50
EGAD00001000365	In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.	Illumina MiSeq	7
EGAD00001000396	We performed serial plasma-Seq analyses on a male who progressed from castration-sensitive to castration-resistant prostate cancer within 10 months following treatment with androgen-deprivation therapy.	Illumina MiSeq	2
EGAD00001000688	In this study we performed ultra deep sequencing of genes associated with anti-EGFR resistance, such as KRAS, BRAF, PIK3CA, and EGFR in 17 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy.	Illumina MiSeq	25
EGAD00001000748	In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy.	Illumina MiSeq	19
EGAD00001000761	In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x)	Illumina MiSeq	14
EGAD00001000762	We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases	Illumina HiSeq 2000	8
EGAD00001000763	We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing	Illumina MiSeq	23
EGAD00001001009	Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X	Illumina HiSeq 2000	4
EGAD00001001010	Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2	Ion Torrent Proton	8
EGAD00001001313	We enriched a panel of cancer associated genes using the Custom Sure Select Target Enrichment Kit. Identified mutations were validated with deep sequencing in order to assess mutated allele frequencies more accurately.	Illumina MiSeq	10
EGAD00001001314	Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61).	Illumina MiSeq	125
EGAD00001002149	Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping in plasma DNA of prostate cancer patients	Illumina MiSeq	95
EGAD00001002150	Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material	Illumina MiSeq	8
EGAD00001002215	Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.	Illumina MiSeq NextSeq 550	108
EGAD00001002216	RNA-Seq on an Ion Torrent Proton of corresponding tumor material of two metastasized breast cancer patients (Breast7, Breast13).	Ion Torrent Proton	2
EGAD00001002217	Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.	Illumina MiSeq	1
EGAD00001002254	Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.	Illumina MiSeq	3
EGAD00001003273	Low-coverage whole genome sequencing for the establishment of genomewide copy number alterations in pleura effusions and respective primary tumors	Illumina MiSeq	20
EGAD00001005343	random whole-genome shotgun sequencing of cfDNA in control samples (NPH*) and late-stage cancer samples. First letter denotes primary cancer tissue (C: Colon, B: Breast, P: Prostate)	Illumina NovaSeq 6000 NextSeq 550	41
EGAD00001005761	Bevacizumab is an approved anti-angiogenic drug for patients with metastasized colorectal cancer (mCRC) targeting VEGF. The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months and acquired resistance mechanisms are greatly unknown. Using plasma DNA, we studied the evolution of tumor genomes in a cohort of patients with mCRC (n=150) and observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of TCGA data (n=619) suggested an association with later stages, which we confirmed by longitudinal plasma analyses. We defined the minimally amplified region and studied the mechanistic consequences of copy number gain of the involved genes. The amplification of one gene, POLR1D, impacted cell proliferation, resulting in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab. In several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with evolution of therapy resistance. Hence, we describe a novel resistance mechanism against a widely applied treatment in mCRC patients which will impact clinical management .	Illumina MiSeq NextSeq 550	38
EGAD00001005804	Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort)	Illumina MiSeq NextSeq 550	117
EGAD00001005805	Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma from self-reporting healthy individuals (MonRec Cohort)	NextSeq 550	22
EGAD00001005806	Mutation analysis of 10 frequently mutated genes in renal cell carcinoma (BAP1, KDM5C, MET, MTOR, PBRM1, PIK3CA, PTEN, SETD2, TP53, VHL) in plasma DNA of RCC patients using a custom QIASeq panel (MonRec Cohort)	Illumina MiSeq NextSeq 550	276
EGAD00001005812	Whole exome sequencing (WES) of tumor tissues from RCC patients (DIAMOND cohort)	Illumina HiSeq 4000	74
EGAD00001005813	A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.	Illumina HiSeq 4000	62
EGAD00001005814	Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma and urine from RCC patients (DAIMOND cohort)	Illumina HiSeq 4000	106
EGAD00001005815	Paired end shallow whole genome sequencing (sWGS) data of tumor tissue from RCC patients (DAIMOND cohort)	Illumina HiSeq 4000	45
EGAD00001006101	Paired end (47/98) and single end (51/98) shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of colorectal cancer (CRC) patients.	Illumina MiSeq NextSeq 550	52
EGAD00001006103	Mutation analysis of 17 genes (ALK, APC, BRAF, BRCA1, BRCA2, DPYD, EGFR, ERBB2, KIT, KRAS, MET, NRAS, PDGFRA, RET, ROS1, TP53, UGT1A1) in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit.	NextSeq 550	26
EGAD00001006104	Mutation analysis in plasma samples with low ctDNA levels using a molecular barcoding technology, i.e. the single target approach SiMSen-seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing).	Illumina MiSeq NextSeq 550	53
EGAD00001006105	Targeted deep sequencing for the KRAS p.Gly12Asp, p.Gly12Val and p.Ala146Thr mutations in plasma samples of CRC patients.	Illumina MiSeq	27
EGAD00001006288	This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-Seq) for calling of somatic copy number alterations as well as focal amplifications and deletions from patients with breast, colorectal and non-small cell lung cancer.	Illumina MiSeq NextSeq 550	48
EGAD00001006301	The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.	NextSeq 550	48
EGAD00001006384	Shallow whole-genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of metastatic colorectal cancer patients (mCRC).	Illumina MiSeq NextSeq 550	45
EGAD00001006385	Modified Fast Aneuploidy Screening Test-Sequencing System (mFAST-SeqS) was applied to stratify samples based on their overall tumor fraction in cfDNA.	Illumina MiSeq	59
EGAD00001006386	All baseline samples and when available EOT were processed for high-resolution mutation analysis. We designed a SureSelectXT-HS custom panel (Agilent) covering 68 genes with a total size of 260kb using the Agilent SureDesign platform.	NextSeq 550	44
EGAD00001006895	Paired end whole exome sequencing (WES) data of tumor/normal pairs (sorted malignant CD3+/Vb+ T-cells and CD19+ non-malignant B-cells) for the identification of somatic mutation.	NextSeq 550	12
EGAD00001006897	Simple, Multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing (SiMSen-Seq) of 11 PIK3CA hotspot mutations in plasma DNA of breast cancer patients.ng	Illumina MiSeq NextSeq 550	66
EGAD00001006901	Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fraction and ploidy sorted malignant CD3+/Vb+ T-cells and corresponding CD19+ non-malignant B-cells	NextSeq 550	11
EGAD00001007505	This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-seq) for calling of somatic copy number alterations as well as focal amplifications from patients with lung cancer.	Illumina MiSeq NextSeq 550	1